Approaches to Assay Processing Package Validation
Ellis Hughes
Fred Hutch Cancer Research Center - SCHARP - VISC
rstudio::conf(2020L)
Outline
- Fred Hutch and SCHARP
- Assay Pipelines
- Validation
Fred Hutch and SCHARP
Blood Stem Cell Transplantation
and Immunotherapy
Cancer Risk Factors, and Causes,
Prevention and Outcomes
Vaccine Development
and Virus-Associated Cancers
Molecular Underpinnings of Cancer
Tumor-Specific Translational Research
- Established 1992
- Worldwide-impact in the fight against cancer,
HIV/AIDS and other infectious diseases. - Clinical Data Management
- Laboratory Data Management
- Statistical Support and Analysis
Assay Processing Pipelines
image source: https://storage.needpix.com/rsynced_images/crowd-2045498_1280.jpg
Validation
Write Specifications
Code
Design Test Cases
Evaluate Test Cases
Document Results for Final Sign Off
Specifications
Do:
- Set the goals of the project
- Define current state
- Specific Features
- System agnostic
- Define success
- Set a time line
Dont:
- Leave ambiguity final product
- Define exact process
- Leave Success metrics up to interpretation
Documentation
1 Specification Family : 1 file
Record pertinent information
-
Detail
- Spec
- Measureables
- success
#' @title Function Specifications 001
#' @section Last updated by:
#' Ellis Hughes
#' @section Last updated date:
#' 2020-1-27
#'
+ _Specifications_
+ 1.1 Presentation must explain validation procedure.
+ 1.2 Be entertaining.
+ 1.3 Inform and document each step necessary for success.
+ 1.4 Fame and Glamour.
Code
- GitHub and Code Review
- Unit Testing - Testthat
- Roxygen
Test Cases
- Specifically test that Code meets Specs
- Detailed without writing code
- Resolves interpretation errors and improves code
Test Cases
- Test that format
- Combine with Roxygen comments
- Breaking out
- each family of tests into a file
- each sub-test as a testthat case
Final Document
Record All elements in a single location
-
Following good programming practices led to
- Scraping functions for author/edits
- separating out specs into files allows for modular extension
- Roxygen to document editing and edit dates
- using testthat like structure led to ability to using testthat reports to document success/failures
- Automation is mo betta
Final Document
Many thanks to all involved
Fred Hutch, Managers, and Team
